chr19-10124423-G-C

Variant names:

• chr19-10124423-G-C
• rs11085587

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.482 in 151,892 control chromosomes in the GnomAD database, including 17,859 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (17859 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73215 AN: 151774 Hom.: 17868 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.513

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.482 AC: 73233 AN: 151892 Hom.: 17859 Cov.: 31 AF XY: 0.482 AC XY: 35790 AN XY: 74196

African (AFR) AF: 0.458 AC: 18971 AN: 41446

American (AMR) AF: 0.509 AC: 7769 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1714 AN: 5154

South Asian (SAS) AF: 0.500 AC: 2412 AN: 4820

European-Finnish (FIN) AF: 0.483 AC: 5074 AN: 10514

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.502 AC: 34102 AN: 67928

Other (OTH) AF: 0.508 AC: 1071 AN: 2110

Alfa AF: 0.494 Hom.: 2271

Bravo AF: 0.486

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		0.064

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11085587; hg19: chr19-10235099;